class: top, left, inverse, title-slide .title[ # Decomposing temporal changes of biodiversity to loss, survival, and recruitment of individuals: analysis of the North-American avifauna ] .author[ ###
François Leroy
Marta Jarzyna
Petr Keil ] .institute[ ###
Czech University of Life Sciences
Prague ] --- # Temporal change of biodiversity * Multi-faceted phenomenon (species richness, turnover, abundance) * Changes through time * Perturbed by human activities -- .center[ ## Abundance ] * sensitive indicator of biodiversity state * average decline of relative abundance `\(\rightarrow\)` 69% (*acc.* Living Planet Index) .center[ `\(\Rightarrow\)` Marine Sharks and Rays: -71%<br><br> `\(\Rightarrow\)` Freshwater: -83%<br><br> `\(\Rightarrow\)` -3 billion North-American birds since 70's ] --- # Decomposing abundance change * Temporal change of abundance ( `\(\Delta N\)` ) results of `\(3\)` processes <br> .center[ <img src="data:image/png;base64,#images/deltaN_concept1.png" width="100%" /> ] -- <br> `$$\Rightarrow \Delta N = N_{t1} - N_{t0} = R - L$$` <br> `$$\Rightarrow \Delta^2N = \Delta R - \Delta L$$` --- # Decomposing growth rate * Growth rate: per individual average change <br> `$$\Rightarrow \frac{\Delta N}{N_{t0}} = \frac{R}{N_{t0}} - \frac{L}{N_{t0}}$$` -- <br><br> .pull-left[ * Recruitment rate `\(= \frac{R}{N_{t0}}\)` * Recruitment rate = individual probability of producing an individual ] .pull-right[ * Loss rate `\(= \frac{L}{N_{t0}}\)` * Loss rate = individual probability of dying/emigrating ] --- class: inverse, center, middle ## Problem `\(\Rightarrow\)` Assessing the ongoing decrease of abundance does not tell us how loss and recruitment change through time -- `\(\Rightarrow\)` Decrease in recruitment `\(\neq\)` Increase in loss, but they both result in an acceleration of the decrease of abundance -- <br><br> ### From a conservation perspective `\(\rightarrow\)` measures to "bend the curve" of recruitment (*e.g.* working on reproductive sucess, protecting breeding habitat) `$$\neq$$` `\(\rightarrow\)` measures to "bend the curve" of loss (*e.g.* reduction of threats, increasing habitat quality) --- class: inverse, center, middle ## For North-American avifauna, we assessed: ### 1) temporal change of abundance, recruitment and loss from 1987 and 2021 -- ### 2) temporal change of growth rate, recruitment rate and loss rate -- ### 3) which process (recruitment or loss) is driving temporal change of biodiversity --- # Data - Breeding Bird Survey (BBS) .pull-left[ * Structured data on North American avifauna * From 1987 to 2021 ] .pull-right[ * More than 1000 routes * 564 species ] .center[ <img src="data:image/png;base64,#images/map_routes.jpg" width="70%" /> ] --- # Model - Dail & Madsen .pull-left[ * Stacked hierarchical model ] .pull-right[ * Bayesian framework ] <br> `$$N_{t+1} = Survival_{t+1} + Recruitment_{t+1}$$` .center[ #### with ] `$$Survival_{t+1} \sim Bin(N_t, \omega)$$` `$$Recruitment_{t+1} \sim Poisson(\gamma)$$` .footnote[ **Note:** `\(Loss_t = N_t - S_{t+1}\)` ] -- * Accounting for detection probabilities, depending on meteorological covariates: `$$N^*{_t} \sim Bin(N_t, p)$$` .center[ `\(\Rightarrow\)` **Sky condition, wind condition, temperature** & **time of the day** ] --- # Model - Dail & Madsen * 1 MCMC chain (= 1 core) with 100 000 iterations `\(\sim\)` **2 days** * 3 chains per species `\(\times\)` 564 species `\(\Rightarrow\)` **1692 MCMC chains** <br><br> .center[ `\(\Rightarrow\)` **9.3 years** to fit the model using 1 core ( `\(\sim\)` 1 year using 8 cores) ] -- <br><br> .center[ `\(\Rightarrow\)` Ohio SuperComputer to parallelize the learning on **1692 cores** <br> <img src="data:image/png;base64,#images/OSC_logo.png" width="768" /> ] --- # Change in abundance, recruitment and loss -- .center[ <img src="data:image/png;base64,#images/map_ab.jpg" width="100%" /> ] --- # Change in abundance, recruitment and loss .center[ <img src="data:image/png;base64,#images/map_rec.jpg" width="100%" /> ] --- # Change in abundance, recruitment and loss .center[ <img src="data:image/png;base64,#images/map_loss.jpg" width="100%" /> ] --- # Change in abundance, recruitment and loss .center[ <img src="data:image/png;base64,#images/map_all_number.jpg" width="90%" /> ] --- # Recruitment vs. Loss .center[ <img src="data:image/png;base64,#images/recVsLoss1.png" width="75%" /> ] --- # Recruitment vs. Loss .center[ <img src="data:image/png;base64,#images/recVsLoss2.png" width="75%" /> ] --- # Recruitment vs. Loss .center[ <img src="data:image/png;base64,#images/recVsLoss3.png" width="75%" /> ] --- # Recruitment vs. Loss .center[ <img src="data:image/png;base64,#images/recVsLoss4.png" width="75%" /> ] --- # Recruitment vs. Loss .center[ <img src="data:image/png;base64,#images/recVsLoss5.png" width="75%" /> ] --- # Recruitment vs. Loss .center[ <img src="data:image/png;base64,#images/recVsLoss6.png" width="75%" /> ] --- # Recruitment vs. Loss .center[ <img src="data:image/png;base64,#images/recVsLoss7.png" width="75%" /> ] --- # Recruitment vs. Loss .center[ <img src="data:image/png;base64,#images/recVsLoss_ab.png" width="75%" /> ] --- # Recruitment vs. Loss .center[ <img src="data:image/png;base64,#images/recVsLoss9.png" width="75%" /> ] --- # Recruitment vs. Loss .center[ <img src="data:image/png;base64,#images/recVsLoss_colors.png" width="75%" /> ] --- # Recruitment vs. Loss: BBS routes .center[ <img src="data:image/png;base64,#images/recVsLoss.png" width="100%" /> ] --- # Recruitment vs. Loss in space .center[ <img src="data:image/png;base64,#images/map_recVsLoss.png" width="90%" /> ] --- # Recruitment vs. Loss in space (smoothened) .center[ <img src="data:image/png;base64,#images/map_recVsLoss_gam.png" width="90%" /> ] --- # Change in growth, recruitment and loss rates .center[ <img src="data:image/png;base64,#images/map_gr.png" width="100%" /> ] --- # Change in growth, recruitment and loss rates .center[ <img src="data:image/png;base64,#images/map_recRate.png" width="90%" /> ] --- # Change in growth, recruitment and loss rates .center[ <img src="data:image/png;base64,#images/map_lossRate.png" width="90%" /> ] --- # Change in growth, recruitment and loss rates .center[ <img src="data:image/png;base64,#images/map_rates_all.png" width="90%" /> ] --- # Recruitment rate vs. Loss rate .center[ <img src="data:image/png;base64,#images/recRVsLossR1.png" width="75%" /> ] --- # Recruitment rate vs. Loss rate .center[ <img src="data:image/png;base64,#images/recRVsLossR2.png" width="75%" /> ] --- # Recruitment rate vs. Loss rate .center[ <img src="data:image/png;base64,#images/recRVsLossR3.png" width="75%" /> ] --- # Recruitment rate vs. Loss rate .center[ <img src="data:image/png;base64,#images/recRVsLossR4.png" width="75%" /> ] --- # Recruitment rate vs. Loss rate .center[ <img src="data:image/png;base64,#images/recRVsLossR.png" width="100%" /> ] --- # Recruitment rate vs. Loss rate in space .center[ <img src="data:image/png;base64,#images/map_recRVsLossR.png" width="90%" /> ] --- # Recruitment rate vs. Loss rate (smoothened) .center[ <img src="data:image/png;base64,#images/map_recRVsLossR_gam.png" width="90%" /> ] --- # Species' preferred habitat - Numbers <br><br> .center[ <img src="data:image/png;base64,#images/barplots_number.png" width="100%" /> ] --- # Species' preferred habitat - Rates <br><br> .center[ <img src="data:image/png;base64,#images/barplots_rate.png" width="100%" /> ] --- # Conclusion .pull-left[ * At the **community level**: decrease in the number of extinction and recruitment drive biodiversity change ] .pull-right[ <img src="data:image/png;base64,#images/recVsLoss.png" width="95%" /> ] -- .pull-left[ **In fact:** <br> * At the **individual level**: increase in recruitment and extinction rate are driving the population dynamic ] .pull-right[ <img src="data:image/png;base64,#images/recRVsLossR.png" width="95%" /> ] --- # Conclusion `\(\Rightarrow\)` From a conservation perspective, working at the individual level is the most important <br> `\(\Rightarrow\)` Focus must be done on bending the loss rate curve (*e.g.* habitat loss, fragmentation, predation by domestic animals...) .center[ <img src="data:image/png;base64,#images/recRVsLossR.png" width="60%" /> ] --- class: inverse, center, middle # Thank you for your attention <br><br><br> <svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:white;height:1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M464 64H48C21.49 64 0 85.49 0 112v288c0 26.51 21.49 48 48 48h416c26.51 0 48-21.49 48-48V112c0-26.51-21.49-48-48-48zm0 48v40.805c-22.422 18.259-58.168 46.651-134.587 106.49-16.841 13.247-50.201 45.072-73.413 44.701-23.208.375-56.579-31.459-73.413-44.701C106.18 199.465 70.425 171.067 48 152.805V112h416zM48 400V214.398c22.914 18.251 55.409 43.862 104.938 82.646 21.857 17.205 60.134 55.186 103.062 54.955 42.717.231 80.509-37.199 103.053-54.947 49.528-38.783 82.032-64.401 104.947-82.653V400H48z"></path></svg> leroy@fzp.czu.cz <svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:lightblue;height:2em;" xmlns="http://www.w3.org/2000/svg"> <path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"></path></svg> @FrsLry <svg viewBox="0 0 496 512" style="position:relative;display:inline-block;top:.1em;fill:white;height:2em;" xmlns="http://www.w3.org/2000/svg"> <path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"></path></svg> FrsLry <svg viewBox="0 0 320 512" style="position:relative;display:inline-block;top:.1em;fill:white;height:1em;" xmlns="http://www.w3.org/2000/svg"> <path d="M302.189 329.126H196.105l55.831 135.993c3.889 9.428-.555 19.999-9.444 23.999l-49.165 21.427c-9.165 4-19.443-.571-23.332-9.714l-53.053-129.136-86.664 89.138C18.729 472.71 0 463.554 0 447.977V18.299C0 1.899 19.921-6.096 30.277 5.443l284.412 292.542c11.472 11.179 3.007 31.141-12.5 31.141z"></path></svg> https://frslry.github.io/ --- # Per species change - Abundance <img src="data:image/png;base64,#images/perSpecies_ab.png" width="2267" /> --- # Per species change - Recruitment <img src="data:image/png;base64,#images/perSpecies_rec.png" width="2268" /> --- # Per species change - Loss <img src="data:image/png;base64,#images/perSpecies_loss.png" width="2276" /> --- # Per species change - Growth rate <img src="data:image/png;base64,#images/perSpecies_gr.png" width="2268" /> --- # Per species change - Recruitment rate <img src="data:image/png;base64,#images/perSpecies_recR.png" width="2268" /> --- # Per species change - Loss rate <img src="data:image/png;base64,#images/perSpecies_lossR.png" width="2268" /> --- # Rec. vs. Loss colored by ab. trend <img src="data:image/png;base64,#images/rec_vs_loss_colored.png" width="2328" /> --- # Rec. rate vs. Loss rate colored by growth rate <img src="data:image/png;base64,#images/recR_vs_lossR_colored.png" width="2328" />